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- PDB-6ibd: The Phosphatase and C2 domains of Human SHIP1 -

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Basic information

Entry
Database: PDB / ID: 6ibd
TitleThe Phosphatase and C2 domains of Human SHIP1
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
KeywordsHYDROLASE / Phosphatidylinositol phosphate phosphatase / Alzheimer's Disease
Function / homology
Function and homology information


inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ...inositol-polyphosphate 5-phosphatase / negative regulation of neutrophil differentiation / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-1,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / negative regulation of monocyte differentiation / phosphatidylinositol dephosphorylation / negative regulation of immune response / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / negative regulation of bone resorption / positive regulation of B cell differentiation / Synthesis of IP3 and IP4 in the cytosol / negative regulation of B cell proliferation / negative regulation of osteoclast differentiation / PECAM1 interactions / Synthesis of PIPs at the plasma membrane / negative regulation of interleukin-6 production / regulation of immune response / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / negative regulation of signal transduction / positive regulation of erythrocyte differentiation / determination of adult lifespan / SH3 domain binding / Signaling by CSF1 (M-CSF) in myeloid cells / Downstream TCR signaling / T cell receptor signaling pathway / cytoskeleton / intracellular signal transduction / positive regulation of apoptotic process / membrane raft / apoptotic process / signal transduction / plasma membrane / cytosol
Similarity search - Function
Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBradshaw, W.J. / Williams, E.P. / Fernandez-Cid, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: Structure / Year: 2024
Title: Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2.
Authors: Bradshaw, W.J. / Kennedy, E.C. / Moreira, T. / Smith, L.A. / Chalk, R. / Katis, V.L. / Benesch, J.L.P. / Brennan, P.E. / Murphy, E.J. / Gileadi, O.
History
DepositionNov 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1


Theoretical massNumber of molelcules
Total (without water)52,8781
Polymers52,8781
Non-polymers00
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.889, 80.076, 90.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 / Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 / SH2 domain-containing inositol 5'- ...Inositol polyphosphate-5-phosphatase of 145 kDa / SIP-145 / SH2 domain-containing inositol 5'-phosphatase 1 / SHIP-1 / p150Ship / hp51CN


Mass: 52877.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5D, SHIP, SHIP1 / Plasmid: pGTVL2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92835, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M bis-tris, 14% (w/v) PEG 2000 MME, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.48→80.08 Å / Num. obs: 76674 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.062 / Rrim(I) all: 0.197 / Χ2: 0.96 / Net I/σ(I): 11.4
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 13.3 % / Rmerge(I) obs: 3.948 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3736 / CC1/2: 0.385 / Rpim(I) all: 1.639 / Rrim(I) all: 4.289 / Χ2: 0.87 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OKM

5okm


Resolution: 1.48→59.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.379 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20054 2057 2.7 %RANDOM
Rwork0.17309 ---
obs0.17385 74516 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.726 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.48→59.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 0 372 3991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173527
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.6455262
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5718261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46723.45200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53315696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8151516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0781.8711836
X-RAY DIFFRACTIONr_mcbond_other2.0621.8691835
X-RAY DIFFRACTIONr_mcangle_it3.1192.8022303
X-RAY DIFFRACTIONr_mcangle_other3.1192.8032304
X-RAY DIFFRACTIONr_scbond_it3.0942.182022
X-RAY DIFFRACTIONr_scbond_other3.0932.182022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.813.1262937
X-RAY DIFFRACTIONr_long_range_B_refined6.39122.1354277
X-RAY DIFFRACTIONr_long_range_B_other6.35221.754199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 135 -
Rwork0.275 5428 -
obs--99.71 %

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